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[ADAM-1093] Move to support Spark 2.0.0.
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Relies on bigdatagenomics/utils#78. Resolves bigdatagenomics#1093:

* Clean up logging in VariantContextRDD
* Add move_to_spark_2.sh script and CI hooks
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fnothaft committed Aug 24, 2016
1 parent eb6f2e4 commit e4a539c
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Showing 4 changed files with 17 additions and 2 deletions.
Expand Up @@ -18,7 +18,6 @@
package org.bdgenomics.adam.rdd.variation

import org.apache.hadoop.io.LongWritable
import org.apache.spark.Logging
import org.apache.spark.rdd.RDD
import org.bdgenomics.adam.converters.VariantContextConverter
import org.bdgenomics.adam.models.{
Expand All @@ -28,6 +27,7 @@ import org.bdgenomics.adam.models.{
}
import org.bdgenomics.adam.rdd.MultisampleGenomicRDD
import org.bdgenomics.formats.avro.Sample
import org.bdgenomics.utils.misc.Logging
import org.bdgenomics.utils.cli.SaveArgs
import org.seqdoop.hadoop_bam._

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2 changes: 1 addition & 1 deletion pom.xml
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<hadoop-bam.version>7.6.0</hadoop-bam.version>
<slf4j.version>1.7.21</slf4j.version>
<bdg-formats.version>0.9.0</bdg-formats.version>
<bdg-utils.version>0.2.7</bdg-utils.version>
<bdg-utils.version>0.2.8-SNAPSHOT</bdg-utils.version>
<htsjdk.version>2.5.0</htsjdk.version>
</properties>

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7 changes: 7 additions & 0 deletions scripts/jenkins-test
Expand Up @@ -28,6 +28,13 @@ then
exit 1
fi

# are we testing for spark 2.0.0? if so, we need to rewrite our poms first
if [ ${SPARK_VERSION} == 2.0.0 ];
then
echo "Rewriting POM.xml files for Scala 2.10."
./scripts/move_to_spark_2.sh
fi

# are we testing for scala 2.11? if so, we need to rewrite our poms to 2.11 first
if [ ${SCALAVER} == 2.11 ];
then
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8 changes: 8 additions & 0 deletions scripts/move_to_spark_2.sh
@@ -0,0 +1,8 @@
#!/bin/bash

set +x

find . -name "pom.xml" -exec sed -e "/utils-/ s/_2.10/-spark2_2.10/g" \
-e "/adam-/ s/_2.10/-spark2_2.10/g" \
-e "/spark.version/ s/1.6.1/2.0.0/g" \
-i .spark2.bak '{}' \;

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